BACKGROUND: Our study examines the relationship between gastroesophageal reflux disease (GERD) and small intestinal bacterial overgrowth (SIBO), focusing on the potential impact of acid-suppressive drugs. We also explore changes in gut microbiota and metabolism in patients with both conditions. METHODS: This study included patients from the Department of Gastroenterology, Beijing Shijitan Hospital, between February 2021 and November 2023. All patients underwent assessments including questionnaires, hydrogen and methane breath tests, and gastroscopy. GERD was diagnosed using the GERD-Q scale and gastroscopy, while SIBO was diagnosed via breath tests. We analyzed the correlation between GERD and SIBO, identified risk factors for SIBO, and examined the gut microbiota using 16S rRNA sequencing to explore the relationship between GERD and SIBO. RESULTS: The retrospective study included 394 patients.148 with GERD and 287 with positive SIBO results. Among these, 270 had a positive methane (CH) breath test and 97 had a positive hydrogen (H) breath test. GERD was more common in patients with positive SIBO (P = 0.007), and the link between CH breath tests and GERD was stronger than that with H breath tests (P = 0.020). Logistic regression showed GERD is an independent risk factor for SIBO. Short-term, low-dose acid-suppressive drugs did not affect SIBO development. 16S rRNA sequencing of fecal microbiota from 24 patients showed dominant microbiota in SIBO-positive GERD patients included and . Patients with both GERD and SIBO had differential metabolites, mainly associated with ATP-Binding Cassette transporters (ABC transporters). CONCLUSION: GERD is strongly linked to SIBO, especially in patients with a positive CH breath test. The gut microbiota in GERD and SIBO patients differs from healthy individuals, with as a key marker. Metabolic changes are mainly related to ABC transporter metabolites.